Notebooks

Notebooks in Albert Invent are a tool for organizing your laboratory work in a centralized, secure place that is connected to other parts of the Albert platform. They allow you to capture unstructured notes and data, attachments, images, and documents within Projects, set up complex synthesis instructions, document Standard Operating Procedures (SOPs), and collaborate with team members.

Create a notebook

Create an empty notebook

from albert import Albert
from albert.resources.notebooks import Notebook

client = Albert.from_client_credentials()

notebook = Notebook(parent_id="PRJ123", name="Reaction Notes")
notebook = client.notebooks.create(notebook=notebook)

Add different block types

Add header, paragraph, checklist, table, image, and attachment blocks

from pathlib import Path

from albert import Albert
from albert.resources.notebooks import (
    AttachesBlock,
    AttachesContent,
    ChecklistBlock,
    ChecklistContent,
    ChecklistItem,
    HeaderBlock,
    HeaderContent,
    ImageBlock,
    ImageContent,
    ParagraphBlock,
    ParagraphContent,
    TableBlock,
    TableContent,
)

client = Albert.from_client_credentials()

notebook = client.notebooks.get_by_id(id="NTB123")

# Provide a file path to upload for image and attachment blocks.
image_path = Path("/path/to/image.png")
image_block = ImageBlock(content=ImageContent(file_path=image_path, with_background=True))
attaches_block = AttachesBlock(content=AttachesContent(file_path=image_path))

notebook.blocks = [
    HeaderBlock(content=HeaderContent(level=2, text="Notebook overview")),
    ParagraphBlock(content=ParagraphContent(text="Run conditions and observations.")),
    ChecklistBlock(
        content=ChecklistContent(
            items=[
                ChecklistItem(checked=False, text="Prepare reagents"),
                ChecklistItem(checked=True, text="Start reaction"),
            ]
        )
    ),
    TableBlock(
        content=TableContent(
            content=[
                ["Reagent", "Mass (mg)"],
                ["A", "10"],
                ["B", "25"],
            ],
            with_headings=True,
        )
    ),
    image_block,
    attaches_block,
]

notebook = client.notebooks.update_block_content(notebook=notebook)

Note

When file_path is set on image or attachment content, the SDK uploads the file and fills in file_key, format, and (for attachments) title.

Add a Ketcher block

Create a new Ketcher block with SMILES

from albert import Albert
from albert.resources.notebooks import KetcherBlock, KetcherContent

client = Albert.from_client_credentials()

notebook = client.notebooks.get_by_id(id="NTB123")
notebook.blocks.append(
    KetcherBlock(content=KetcherContent(smiles="CCO"))
)
notebook = client.notebooks.update_block_content(notebook=notebook)

Warning

Updating existing Ketcher blocks is not supported. To change a Ketcher block, remove it from notebook.blocks and add a new Ketcher block with the desired smiles.

Replace a Ketcher block

Delete the old Ketcher block and add a new one

from albert import Albert
from albert.resources.notebooks import KetcherBlock, KetcherContent

client = Albert.from_client_credentials()

notebook = client.notebooks.get_by_id(id="NTB123")

# Drop existing Ketcher blocks (this deletes them on update).
notebook.blocks = [b for b in notebook.blocks if b.type != "ketcher"]

# Add a new Ketcher block.
notebook.blocks.append(
    KetcherBlock(content=KetcherContent(smiles="C1=CC=CC=C1"))
)

notebook = client.notebooks.update_block_content(notebook=notebook)

Copy a notebook

Copy a notebook to another parent

from albert import Albert
from albert.resources.notebooks import NotebookCopyInfo, NotebookCopyType

client = Albert.from_client_credentials()

copy_info = NotebookCopyInfo(id="NTB123", parent_id="PRJ456")
notebook_copy = client.notebooks.copy(
    notebook_copy_info=copy_info,
    type=NotebookCopyType.PROJECT,
)
print(notebook_copy.id)